[BioC] bug report for GenomeGraphs

[steffen at stat.Berkeley.EDU]

Dear Paolo,

You should be able to use GenomeGraphs again using biomaRt 1.99.1 and
GenomeGraphs 1.3.3 which both can be downloaded here:

http://bioconductor.org/checkResults/2.4/bioc-LATEST/

Note that these are the developmental versions of these packages.  The
release version of GenomeGraphs should also be fixed (version 1.2.1) but
this is not yet available from the BioC site (should be within the next 12
hours).

Also note that the release branch of biomaRt should be used with the
release version of GenomeGraphs and the devel version of biomaRt should be
used when using the devel version of GenomeGraphs.

Cheers,
Steffen

> Dear Dr. Durinck,
>
> Below It is my outputs on a linuxbox:
>
> Linux valis 2.6.25-gentoo-r7 #2 SMP Wed Nov 5 17:56:30 CET 2008 x86_64
> Intel(R) Xeon(TM) CPU 3.40GHz GenuineIntel GNU/Linux
>
> R version 2.8.0 (2008-10-20)
> Copyright (C) 2008 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>  > library(GenomeGraphs)
> Loading required package: biomaRt
> Loading required package: grid
>  > mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> Checking attributes and filters ... ok
>  > gene <- makeGene(id = "ENSG00000095203",type = "ensembl_gene_id",
> biomart = mart)
>                                                                           V1
> 1 Query ERROR: caught BioMart::Exception::Usage: Attribute biotype NOT
> FOUND
> Error in getBM(c("structure_gene_stable_id",
> "structure_transcript_stable_id",  :
>   Number of columns in the query result doesn't equal number of
> attributes in query.  This is probably an internal error, please report.
>
> and a macbook with Mac OS X 10.5.6 "Leopard":
> R version 2.8.1 (2008-12-22)
> Copyright (C) 2008 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>   Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>  > library("GeneGraph")
> Error in library("GeneGraph") : there is no package called 'GeneGraph'
>  > library("GenomeGraphs")
> Loading required package: biomaRt
> Loading required package: grid
>  > data("exampleData", package="GenomeGraphs")
>  >
>  > minbase = min(probestart)
>  > maxbase = max(probestart)
>  >
>  > mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")
> Checking attributes and filters ... ok
>  > genesplus = new("GeneRegion", start = minbase, end = maxbase, strand
> = "+", chromosome = "3", biomart=mart)
>                                                                           V1
> 1 Query ERROR: caught BioMart::Exception::Usage: Attribute biotype NOT
> FOUND
> Error in getBM(c("structure_gene_stable_id",
> "structure_transcript_stable_id",  :
>   Number of columns in the query result doesn't equal number of
> attributes in query.  This is probably an internal error, please report.
>  >
>
>
>
> Sorry if  You are the wrong person to submit a bug report.
>
>
> Regards,
> Paolo
>